If the File System is used for storing content and metadata, the content of the Master or Child Publications will be over written.
To account for this, set explicit settings for metadata in cd_storage_conf.xml, to ensure that all metadata does not go to the same storage location, for example:
<Storage Type="filesystem" Class="com.tridion.storage.filesystem.FSDAOFactory" Id="defaultFile" defaultFilesystem="false">
<Root Path="c:\published\localFileSystem" />
</Storage>
<Storage Type="filesystem" Class="com.tridion.storage.filesystem.FSDAOFactory" Id="defaultDataFile" defaultFilesystem="true" defaultStorage="true">
<Root Path="c:\published\localFileSystem\data" />
</Storage>
<ItemTypes defaultStorageId="defaultFile" cached="false">
<!-- Query type mapping is replacement for Query gnenerator. If there was query generator defined in a Broker configuration then Query type mapping should be binded to default DB. -->
<Item typeMapping="Query" storageId="defaultdb"/>
<Item typeMapping="PageMeta" cached="true" storageId="defaultDataFile"/>
<Item typeMapping="ComponentPresentationMeta" cached="true" storageId="defaultDataFile"/>
<Item typeMapping="ComponentMeta" cached="true" storageId="defaultDataFile"/>
</ItemTypes>